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LITERATURE CITED

  • Arbogast, B. S., S. V. Edwards, J. Wakeley, P. Beerli, and J. B. Slowinski. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annu. Rev. Ecol. Syst. 33:707740.
  • Arbogast, B. S., S. V. Drovetski, R. L. Curry, P. T. Boag, G. Seutin, P. R. Grant, B. R. Grant, and D. J. Anderson. 2006. The origin and diversification of Galapagos mockingbirds. Evolution 60:370382.
  • Bird, M. I., D. Taylor, and C. Hunt. 2005. Palaeoenvironments of insular Southeast Asia during the Last Glacial Period: a savanna corridor in Sundaland? Quat. Sci. Rev. 24:22282242.
  • Brown, R. M., and A. Diesmos. In press. The Philippines, biology. Pp. 723732 in R.Gillespie and D.Clague, eds. Encyclopedia of islands. Univ. of California Press, Berkeley , CA .
  • Brown, R. M., and S. I. Guttman. 2002. Phylogenetic systematics of the Rana signata complex of Philippine and Bornean stream frogs: reconsideration of Huxley's modification of Wallace's Line at the Oriental–Australian faunal zone interface. Biol. J. Linn. Soc. 76:393461.
  • Butler, P. M. 1998. Fossil history of shrews in Africa. Pp. 121132 in J. M.Wójcik and M.Wolson, eds. Evolution of shrews. Mammal Research Institute, Polish Academy of Sciences, Białowieża .
  • Corbet, G. B., and J. E. Hill. 1992. The mammals of the Indomalayan region. Oxford Univ. Press, New York .
  • Defant, M. J., R. C. Maury, J.-L. Joron, M. D. Feigenson, J. Leterrier, H. Bellon, D. Jacques, and M. Richard. 1990. The geochemistry and tectonic setting of the northern section of the Luzon arc (the Philippines and Taiwan). Tectonophysics 183:187205.
  • De Queiroz, K. 1998. The general lineage concept of species, species criteria, and the process of speciation: a conceptual unification and terminological recommendations. Pp. 5575 in D. J.Howard and S. H.Berlocher, eds. Endless forms: species and speciation. Oxford Univ. Press, Oxford .
  • Diamond, J. M., and M. E. Gilpin. 1983. Biogeographic umbilici and the origin of the Philippine avifauna. Oikos 41:307321.
  • Dickerson, R. E. 1928. Distribution of life in the Philippines. Philippine Bureau of Science, Manila .
  • Dubey, S., N. Salamin, S. D. Ohdachi, P. Barriere, and P. Vogel. 2007. Molecular phylogenetics of shrews (Mammalia: Soricidae) reveal timing of transcontinental colonizations. Mol. Phylogenet. Evol. 44:126137.
  • Dubey, S., N. Salamin, M. Ruedi, P. Barriere, M. Colyn, and P. Vogel. 2008. Biogeographic origin and radiation of the Old World crocidurine shrews (Mammalia: Soricidae) inferred from mitochondrial and nuclear genes. Mol. Phylogenet. Evol. 48:953963.
  • Esselstyn, J. A., P. Widmann, and L. R. Heaney. 2004. The mammals of Palawan Island, Philippines. Proc. Biol. Soc. Wash. 117:271302.
  • Esselstyn, J. A., H. J. D. Garcia, M. G. Saulog, and L. R. Heaney. 2008. A new species of Desmalopex (Pteropodidae) from the Philippines, with a phylogenetic analysis of the Pteropodini. J. Mammal. 89:215225.
  • Evans, B. J., J. C. Morales, J. Supriatna, and D. J. Melnick. 1999. Origin of the Sulawesi macaques (Cercopithecidae: Macaca) as suggested by mitochondrial DNA phylogeny. Biol. J. Linn. Soc. 66:539560.
  • Evans, B. J., R. M. Brown, J. A. McGuire, J. Supriatna, N. Andayani, A. Diesmos, D. Iskandar, D. J. Melnick, and D. C. Cannatella. 2003a. Phylogenetics of fanged frogs: testing biogeographical hypotheses at the interface of the Asian and Australian faunal zones. Syst. Biol. 52:794819.
  • Evans, B. J., J. Supriatna, N. Andayani, M. I. Setiadi, D. C. Cannatella, and D. J. Melnick. 2003b. Monkeys and toads define areas of endemism on Sulawesi. Evolution 57:14361443.
  • Evans, B. J., J. A. McGuire, R. M. Brown, N. Andayani, and J. Supriatna. 2008. A coalescent framework for comparing alternative models of population structure with genetic data: evolution of Celebes toads. Biol. Lett. 4:430433.
  • Everett, A. H. 1889. Remarks on the zoogeographical relationships of the island of Palawan and some adjacent islands. Proc. Zool. Soc. Lond. 1889:220228.
  • Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Inc., Sunderland , MA .
  • Filardi, C. E., and R. G. Moyle. 2005. Single origin of a pan-Pacific bird group and upstream colonization of Australasia. Nature 438:216219.
  • Gorog, A. J., M. H. Sinaga, and M. D. Engstrom. 2004. Vicariance or dispersal? Historical biogeography of three Sunda shelf murine rodents (Maxomys surifer, Leopoldamys sabanus and Maxomys whiteheadi). Biol. J. Linn. Soc. 81:91109.
  • Grant, P. R., B. R. Grant, and K. Petren. 2000. The allopatric phase of speciation: the sharp-beaked ground finch (Geospiza difficilis) on the Galapagos islands. Biol. J. Linn. Soc. 69:287317.
  • Hall, R. 1998. The plate tectonics of Cenozoic SE Asia and the distribution of land and sea. Pp. 99131 in R.Hall and J. D.Holloway, eds. Biogeography and geological evolution of SE Asia. Backhuys Publishers, Leiden .
  • Hall, R. 2002. Cenozoic geological and plate tectonic evolution of SE Asia and the SW Pacific: computer-based reconstructions and animations. J. Asian Earth Sci. 20:353434.
  • Haq, B. U., J. Hardenbol, and P. R. Vail. 1987. Chronology of fluctuating sea levels since the Triassic. Science 235:11561167.
  • Heaney, L. R. 1984. Mammalian species richness on islands on the Sunda Shelf, Southeast Asia. Oecologia 61:1117.
  • Heaney, L. R. 1985. Zoogeographic evidence for middle and late Pleistocene land bridges to the Philippine Islands. Mod. Quat. Res. SE Asia 9:127144.
  • Heaney, L. R. 1986. Biogeography of mammals in SE Asia: estimates of rates of colonization, extinction and speciation. Biol. J. Linn. Soc. 28:127165.
  • Heaney, L. R. 1991. A synopsis of climatic and vegetational change in Southeast Asia. Clim. Change 19:5361.
  • Heaney, L. R. 2000. Dynamic disequilibrium: a long-term, large-scale perspective on the equilibrium model of island biogeography. J. Biogeogr. 9:5974.
  • Heaney, L. R., and M. Ruedi. 1994. A preliminary analysis of biogeography and phylogeny of Crocidura from the Philippines. Carnegie Mus. Nat. Hist. Special Publ. 18:357377.
  • Hutterer, R. 2005. Order Soricomorpha. Pp. 220311 in D. E.Wilson and D. M.Reeder, eds. Mammal species of the world. Johns Hopkins Univ. Press, Baltimore , MD .
  • Hutterer, R. 2007. Records of shrews from Panay and Palawan, Philippines, with the description of two new species of Crocidura (Mammalia: Soricidae). Lynx 38:520.
  • Inger, R. I. 1954. Systematics and zoogeography of Philippine Amphibia. Fieldiana: Zool. 33:182531.
  • Irwin, D. M., T. D. Kocher, and A. C. Wilson. 1991. Evolution of the cytochrome-B gene of mammals. J. Mol. Evol. 32:128144.
  • Jansa, S. A., F. K. Barker, and L. R. Heaney. 2006. The pattern and timing of diversification of Philippine endemic rodents: evidence from mitochondrial and nuclear gene sequences. Syst. Biol. 55:7388.
  • Jones, A. W., and R. S. Kennedy. 2008. Evolution in a tropical archipelago: comparative phylogeography of Philippine fauna and flora reveals complex patterns of colonization and diversification. Biol. J. Linn. Soc. 95:620639.
  • Knowles, L. L., and B. C. Carstens. 2007. Delimiting species without monophyletic gene trees. Syst. Biol. 56:887895.
  • Kozak, K. H., D. W. Weisrock, and A. Larson. 2006. Rapid lineage accumulation in a non-adaptive radiation: phylogenetic analysis of diversification rates in eastern North American woodland salamanders (Plethodontidae: Plethodon). Proc. R. Soc. Lond. Ser. B 273:539546.
  • Lunde, D. P., G. G. Musser, and T. Ziegler. 2004. Description of a new species of Crocidura (Soricomorpha: Sorcidae: Crocidurinae) from Ke Go Nature Reserve, Vietnam. Mammal Study 29:2736.
  • Marshall, D. C., K. Slon, J. R. Cooley, K. B. R. Hill, and C. Simon. 2008. Steady Plio–Pleistocene diversification and a 2-million-year sympatry threshold in a New Zealand cicada radiation. Mol. Phylogenet. Evol. 48:10541066.
  • McGuire, J. A., and B. H. Kiew. 2001. Phylogenetic systematics of Southeast Asian flying lizards (Iguania: Agamidae: Draco) as inferred from mitochondrial DNA sequence data. Biol. J. Linn. Soc. 72:203229.
  • McPeek, M. A. 2008. The ecological dynamics of clade diversification and community assembly. Am. Nat. 172:E270284.
  • Meijaard, E., and A. P. M. Van Der Zon. 2003. Mammals of Southeast Asian islands and their late Pleistocene environments. J. Biogeogr. 30:12451257.
  • Miller, G. S. 1910. Descriptions of two new genera and sixteen new species of mammals from the Philippine Islands. Proc. US Nat. Mus. 38:391404.
  • Mittermeier, R. A., P. R. Gil, M. Hoffmann, J. Pilgrim, T. Brooks, C. G. Mittermeier, J. Lamoreux, and G. A. B. Da Fonesca. 2004. Hotspots revisited. CEMEX, Mexico City .
  • Nee, S. 2001. Inferring speciation rates from phylogenies. Evolution 55:661668.
  • Nylander, J. A. A., J. C. Wilgenbusch, D. L. Warren, and D. L. Swofford. 2008. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24:581583.
  • Ohdachi, S. D., M. Hasegawa, M.-A. Iwasa, P. Vogel, T. Oshida, L.-K. Lin, and H. Abe. 2006. Molecular phylogenetics of soricid shrews (Mammalia) based on mitochondrial cytochrome b gene sequences: with special reference to the Soricinae. J. Zool. 270:177191.
  • Olson, L. E., S. M. Goodman, and A. D. Yoder. 2004. Illumination of cryptic species boundaries in long-tailed shrew tenrecs (Mammalia: Tenrecidae: Microgale), with new insights into geographic variation and distributional constraints. Biol. J. Linn. Soc. 83:122.
  • Outlaw, D. C., and G. Voelker. 2008. Pliocene climatic change in insular Southeast Asia as an engine of diversification in Ficedula flycatchers. J. Biogeogr. 35:739752.
  • Ozawa, A., T. Tagami, E. L. Listanco, C. B. Arpa, and M. Sudo. 2004. Initiation and propagation of subduction along the Philippine Trench: evidence from the temporal and spatial distribution of volcanoes. J. Asian Earth Sci. 23:105111.
  • Pesole, G., C. Gissi, A. De Chirico, and C. Saccone. 1999. Nucleotide substitution rate of mammalian mitochondrial genomes. J. Mol. Evol. 48:427434.
  • Phillimore, A. B., and T. D. Price. 2008. Density-dependent cladogenesis in birds. PLOS Biol. 6:483489.
  • Posada, D., and T. R. Buckley. 2004. Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53:793808.
  • Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817818.
  • Price, T. D. 2008. Speciation in birds. Roberts and Company, Greenwood Village , Colorado .
  • Pybus, O. G., and A. Rambaut. 2002. GENIE: estimating demographic history from molecular phylogenies. Bioinformatics 18:14041405.
  • Rabosky, D. L. 2006a. LASER: a maximum likelihood toolkit for detecting temporal shifts in diversification rates from molecular phylogenies. Evol. Bioinf. Online 2006:257260.
  • Rabosky, D. L. 2006b. Likelihood methods for detecting temporal shifts in diversification rates. Evolution 60:11521164.
  • Rabosky, D. L., and I. J. Lovette. 2008. Explosive evolutionary radiations: decreasing speciation or increasing extinction through time? Evolution 62:18661875.
  • Rambaut, A. 1996. Se-Al: sequence alignment editor. Available at http://evolve.zoo.ox.ac.uk/. [Accessed October 10, 2006].
  • Rambaut, A., and A. J. Drummond. 2007. Tracer v1.4. Available at http://beast.bio.ed.ac.uk/Tracer. [Accessed December 15, 2007].
  • Rohling, E. J., M. Fenton, F. J. Jorissen, G. Bertrand, G. Ganssen, and J. P. Caulet. 1998. Magnitude of sea level lowstands of the last 500,000 years. Nature 394:162165.
  • Ronquist, F., and J. P. Huelsenbeck. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:15721574.
  • Ruedi, M. 1995. Taxonomic revision of shrews of the genus Crocidura from the Sunda Shelf and Sulawesi with description of two new species (Mammalia, Soricidae). Zool. J. Linn. Soc. 115:211265.
  • Ruedi, M., M. Auberson, and V. Savolainen. 1998. Biogeography of Sulawesian shrews: testing for their origin with a parametric bootstrap on molecular data. Mol. Phylogenet. Evol. 9:567571.
  • Schluter, D. 2000. The ecology of adaptive radiation. Oxford Univ. Press, New York .
  • Schmitt, L. H., D. J. Kitchener, and R. A. How. 1995. A genetic perspective of mammalian variation and evolution in the Indonesian Archipelago: biogeographic correlates in the fruit bat genus Cynopterus. Evolution 49:399412.
  • Seehausen, O. 2007. Evolution and ecological theory—Chance, historical contingency and ecological determinism jointly determine the rate of adaptive radiation. Heredity 99:361363.
  • Shimodaira, H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst. Biol. 51:492508.
  • Shimodaira, H., and M. Hasegawa. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:12461247.
  • Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:26882690.
  • Steppan, S. J., C. Zawadzki, and L. R. Heaney. 2003. Molecular phylogeny of the endemic Philippine rodent Apomys (Muridae) and the dynamics of diversification in an oceanic archipelago. Biol. J. Linn. Soc. 80:699715.
  • Storch, G., Z. Qiu, and V. S. Zazhigin. 1998. Fossil history of shrews in Asia. Pp. 93120 in J. M.Wójcik and M.Wolson, eds. Evolution of shrews. Mammal Research Institute, Polish Academy of Sciences, Białowieża .
  • Swofford, D. L. 1999. PAUP*4.0. Phylogenetic analysis using parsimony (*and other methods). Sinauer Associates, Sunderland , MA .
  • Voris, H. K. 2000. Maps of Pleistocene sea levels in Southeast Asia: shorelines, river systems and time durations. J. Biogeogr. 27:11531167.
  • Wallace, A. R. 1860. On the zoological geography of the Malay Archipelago. Proc. Linn. Soc. 4:172184.
  • Zachos, J., M. Pagani, L. Sloan, E. Thomas, and K. Billups. 2001. Trends, rhythms, and aberrations in global climate 65 ma to present. Science 292:686693.